Repository navigation
Add levelComplexConcs and getComplexFamilies, and a perComplex option for flexibilizeEnzConcs - #19
Merged
Merged
Conversation
…f flexibilizeEnzConcs (parity#131)
Unit test results63 tests 63 ✅ 10s ⏱️ Results for commit 6a4b905. |
This was referenced Nov 2, 2026
Merged
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
levelComplexConcsgives every enzyme complex one abundance betweenfillEnzConcsandconstrainEnzConcs: per complex it takes the median (or mean) of the measured, owned subunits'concs / MW / copiesand writes backcopies * summary * MW. Unmeasured owned subunits are filled, subunits shared by several complexes keep their measurement, and the result lists what was adjusted, added, skipped and shared.getComplexFamiliesgroups the enzymes of multi-subunit reactions into complexes fromec.rxnEnzMat.flexibilizeEnzConcstakesperComplex(default false): it ranks complexes by the growth gained per fold of raising all their caps and raises all subunits of the chosen complex by one factor, so levelled ratios are kept.The functions behave as
level_complex_concs,complex_familiesandflexibilize_enz_concs(per_complex=True)in geckopy (CompMetEng/geckopy#63). Parity: CompMetEng/raven-gecko-parity#131.